## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not found
Now we combine the TSS-only, the TES-only and the TSS.TES methods for all 5 normalization methods
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only)
found the 5-prime adapters!
## Error in fread(paste0(fig.dir, ".norm_host", "/", norm.method, "_", EndType, :
## File 'LoRTIA_virus/TSS_abund.norm_host/host_read.count_TSS_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
## Error in fread(paste0(fig.dir, ".norm_VST", "/", norm.method, "_", EndType, :
## File 'LoRTIA_virus/TSS_abund.norm_VST/VST_TSS_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
found the 3-prime adapters!
## Error in fread(paste0(fig.dir, ".norm_host", "/", norm.method, "_", EndType, :
## File 'LoRTIA_virus/TES_abund.norm_host/host_read.count_TES_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
## Error in fread(paste0(fig.dir, ".norm_VST", "/", norm.method, "_", EndType, :
## File 'LoRTIA_virus/TES_abund.norm_VST/VST_TES_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
found both 5-prime AND 3-prime adapters!
## Error in fread(paste0(fig.dir, ".norm_host", "/", norm.method, "_", EndType, :
## File 'LoRTIA_virus/TSS.TES_abund.norm_host/host_read.count_TSS.TES_abund.mean.tsv' does not exist or is non-readable. getwd()=='C:/GitHub/EHV-1-dynamic'
## [1] TRUE
## [1] "ORF1"
NA shows the number of genes where the clustering did not yield an unambiguous result.
These pairs were analyzed: ie180/us1, ie180/ep0, us1/ep0, noir1/noir2, noir1/ie180, noir2/ie180